Liam Research 1

geo_name_list = c("GSE129166", "GSE34748", "GSE51675", "GSE15296", "GSE46474", "GSE50084")
geo_list = c(getGEO(filename="Data/GSE129166_series_matrix.txt.gz"), getGEO(filename="Data/GSE34748_series_matrix.txt.gz"), getGEO(filename="Data/GSE51675_series_matrix.txt.gz"), getGEO(filename="Data/GSE15296_series_matrix.txt.gz"), getGEO(filename="Data/GSE46474_series_matrix.txt.gz"), getGEO(filename="Data/GSE50084_series_matrix.txt.gz"))

Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpYzuDYu/GPL570.soft.gz 
Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpYzuDYu/GPL570.soft.gz 
Using locally cached version of GPL570 found here:
C:\Users\lmcca\AppData\Local\Temp\RtmpYzuDYu/GPL570.soft.gz 

for(geo in geo_list) {
  print(fData(geo))
  print(names(which(colSums(is.na(fData(geo)))>0)))
}

character(0)

character(0)

[1] "GENE"    "TIGR_ID"

character(0)

character(0)

character(0)

All gse have a gene symbol column which can be used to match records except for the last one, GSE50084 which has the gene as the 2nd listed element under gene_assignment, and GSE51675 which is missing all of its gene info.

for(geo in geo_list) {
  print(pData(geo))
  print(names(which(colSums(is.na(pData(geo)))>0)))
}

character(0)

character(0)

character(0)

character(0)

character(0)

character(0)

for (geo in geo_list) {
  print(data.frame(t(exprs(geo))))
  print(names(which(colSums(is.na(data.frame(t(exprs(geo)))))>0)))
}

character(0)

character(0)

character(0)

character(0)

character(0)

character(0)

for (geo in geo_list) {
  df = data.frame(t(exprs(geo)))
  boxplot(df[1:100])
}

Plots for GSE51675 and GSE15296 show that they have been transformed somehow. Other than those, the other 4 seem fairly contained between 0-14 expression intensity.

GSE51675 has been discarded due to small sample size, missing info, and transformed expression values. GSE50084 has been discarded

# Contains "GSE129166", "GSE34748"
length(union(fData(geo_list[[1]])["Gene Symbol"], fData(geo_list[[2]])["Gene Symbol"])[[1]])

[1] 54675

# Contains "GSE129166", "GSE46474"
length(union(fData(geo_list[[1]])["Gene Symbol"], fData(geo_list[[5]])["Gene Symbol"])[[1]])

[1] 54675

All 3 have perfect overlap so the datasets recommended for use are “GSE129166”, “GSE34748”, and “GSE46474”

length(union(fData(geo_list[[1]])["Gene Symbol"], fData(geo_list[[4]])["Gene Symbol"])[[1]])

[1] 54675